Commit 870aa989 authored by Jelle Scholtalbers's avatar Jelle Scholtalbers
Browse files

Remove the unneccessary conda activate

parent 70b4424e
Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
Include: software-properties-common
%post
apt update
apt install -y software-properties-common
apt-add-repository universe
apt update
apt install -y wget
apt install -y wget bzip2
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3.sh
bash miniconda3.sh -b -p "$HOME"/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
echo "PATH=$HOME/miniconda/bin:$PATH" >> "$SINGULARITY_ENVIRONMENT"
. ./$HOME/miniconda/bin/activate
bash miniconda3.sh -b -p /opt/miniconda
export PATH="/opt/miniconda/bin:$PATH"
echo "PATH=/opt/miniconda/bin:$PATH" >> "$SINGULARITY_ENVIRONMENT"
conda install -y -c bioconda bwa
%test
export PATH="$HOME/miniconda/bin:$PATH"
export PATH="/opt/miniconda/bin:$PATH"
command -v conda >/dev/null 2>&1 || exit 1
command -v bwa >/dev/null 2>&1 || exit 1
......
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